Smallville  A New Beginning  S1Ep6 Apprentice
by NateTheGreat11
Summary: Clark returns and takes Conner to the Fortress to learn about his heritage. Lois and Chloe begins investigating LuthorCorp's cloning projects, and find Zoe investigating too. Martha helps Lena discover her identity.


**Smallville: A New Beginning**

Episode 6: Apprentice

Conner Kent rolled over in the dirt. That hit he just took was really hard. His blue t-shirt and red plaid shirt were torn up. The raging beast that was Riley Van Horn was no one to be messed with. He was the closest thing to a werewolf Smallville has ever. He was hairy and muscular, and when in his beast form had to walk on all fours. His abilities seemed ridiculous, but with his hairy, monster like appearance came a mighty beast. Riley was strong, fast and deadly, he was an adversary it took Conner awhile to take down. He was the only one of Boomer's crew who was able to escape being arrested, and now he was seeking revenge.

"Marcus! Dawn! Plan on helping?" Conner yelled as Riley pounced on top of him.

No reply. They must have been looking for him. Conner kneed the beast in the stomach, and he flipped him over. Riley rolled, and got back up. He began to run for Conner in powerful leaps. His feet looked as if they hardly touched the ground. Riley's claws grew longer with each step. They were covered in Conner's blood. Conner stood up. He wanted to try and over power the beast. He was in a wrestler's position. He was going to go in for a tackle. He charged forward as Riley came closer. Rather than grab the beast, he grabbed the dirt, as Riley was on his back. Conner felt his claws sink in. No one he's ever known could do him this much damage. He felt the blood wetting his shirt. He rolled over again, but Riley wasn't there. He was incapacitated. He was incapacitated on someone's shoulder. A man in a blue colored once piece suit, with red boots and boxers. An S in a diamond shape, and a red cape flowing like angel wings. His hero had black hair, a lot like Conner's. He was smiling at Conner.

"You handled that a lot quicker than I could" Conner said with a smile on his face

"For what it's worth you stood your ground" The hero said back.

The hero put Riley down on the floor, and he walked up to Conner. The two shook hands.

"Glad to you have you back, Clark." Conner said

"Glad to be back" Clark said to Conner

* * *

><p>Conner sped home after the school day ended. Martha was sitting in the living room with her normal cup of coffee. As Conner walked through the door. Martha gazed upon his clothes.<p>

"Hey Ma." He said

"Hey…Conner" She said curiously. She looked down at her Coffee and then looked back up again. He looked at her curiously. Something must be bothering her.

"Everything okay?" He asked

"Yeah…it's just…Conner, I was thinking long about what I said last night, and letting you join a team of heroes…I don't think it's a good idea." She argued

"…Ma" He was interrupted

"Just, hear me out. Conner you're a 14 year old super-human, who's trying to live a normal life. And now you're Principle wants you to be a secret agent for him, which I don't even think is legal." She said

"Illegal doesn't always mean wrong." He argued

"I know that…but still, it isn't a good idea to put the safety of the students in the hands of other students, and I plan on going down there and talking to him about this." Martha said

"Ma, please, I want to do this. The school needs this." Conner pleaded

"I'm still not sure about this Conner." She said "Plus, why are your clothes scratched up?"

"Meteorite induced Wolf guy…don't ask" He said to her

Martha began to walk away from him. As she reached the window she turned back and looked at him.

"Fine. I guess your right. At least you were able to take him down." She agreed "I doubt thing like that happen everyday anyway."

"Thanks…and Ma, speaking of today…" He told her "Well, I didn't exactly take him down. I was about to, but someone interrupted things…"

"Who?" She asked

At that they heard a knock on the door. Conner sped to the door. He opened it. Clark was there with his glasses on. He was in his casual clothes, rather than his reporter attire. Next to him was Lois. Still as beautiful as Conner remembered. Martha smiled as she looked at who was at the door. Clark and Lois walked inside and hugged her. Conner had missed Clark. He hadn't seen him in 6 months, and didn't even go to his would-be wedding. Clark and Lois were conversing with Martha as Conner looked on. This was the first time his whole family had been together, with him, and he was enjoying the moment. Clark looked toward him and excused himself. He got up and slipped of his glasses and walked toward his little brother. He grabbed Conner by the shoulder.

"So how are you enjoying Smallville High." Clark asked

"It's okay…better when I'm out on the field." Conner replied

"You joined the football team?" Clark asked

"No" Conner replied "I joined a team of young heroes who protect Smallville from metahuman."

"We need to talk" Clark said as he sped for the loft. Conner followed "Fighting metahumans?" Clark asked "I thought you said you weren't ready for that."

"I am ready for that. I'm just not ready to don a suit. I have to do this."

"But Conner, you don't have to do it, it's the reason people like me show our faces, that way people can live their lives without worrying."

"Clark, Martha always tells me how you used to do this in High School, and let's face it for a guy faster than a speeding bullet…you tend to not be around so often."

"There's a reason for that…as I grew up I had a lot of trials I had to face on my own, and I figured you'd have to do the same. I wasn't able to become a hero by taking the easy way out of things."

"So let me protect Smallville, behind closed doors."

"Well since your ready to embrace your destiny there's somewhere you should go first. Conner you know you're a clone, and you know your Kryptonian, but you don't know much about your Kryptonian side. It's about time I take you to meet your real father."

* * *

><p>Lois and Martha were sitting in the Kent Farm, talking.<p>

"So, how's Perry?" Martha asked

"Great. He just became Editor-In-Chief after Tess disappeared." Lois said

"Did you guys ever find out what happened to her?" Martha asked

"No…but I have a hunch. She disappeared right after Lex rose from the dead, there has to be a connection." Lois said

"And Lionel died as Darkseid" Martha added

"Lionel's body disappeared completely, but there's still something I don't understand, Lionel founded a company called PreClox just to resurrect Lex, through cloning. A company like that doesn't just become defunct." Lois added

"You're right, it doesn't." A familiar voice said

Martha and Lois turned toward the door to find a blonde woman. It was Chloe. Both got up from their seats to hug her.

"Chloe…what are you doing…here?"

"Decided to come back down here to see the people I grew up with…and because I had a lead I might need Lois's help with. Speaking of PreClox, I kept watch over that company after Lex returned. But there cloning projects didn't end with Lionel's life, Lex created 3 more clones. Two of them died due to rapid aging, but there was one clone made who was unaccounted for."

"So then what are we waiting for?"

"I was going to have Clark join us…but he must be busy being Superman and all."

"He's busy, but he left with Conner a while ago."

"Probably introducing him to the snow-dad up north."

Someone was knocking at the door. Martha walked up to the door and opened it. Lena was there.

"Hi Lena." Martha said as she hugged Lena.

"Hey Mrs. K"

Lena stopped hugging Martha and looked at the two strangers in Martha's house. They looked familiar.

"Oh, Lena this is Lois Lane and Chloe Sullivan, friends of Clark's" Martha introduced them to eachother.

"Hi, I'm Lena. Lena Luther. With an E."

The ladies shook hands.

"Well Mrs. Kent we'll be back later. Now we have a story to find." Lois said

Lena waved bye to the two as they walked out of the front door.

"So Lena what's on your mind?" Martha asked

"Well, Mrs. K. It's a bit complicated actually"

"How complicated?"

"Well, I want to find out about my past, and I figure, if anyone could help it would be the ex-senator."

"Well, wether or not we can find out who you are depends on what you know."

"Nothing really…Just that Lex Luthor raised me the first couple of days I remembered. My first memory, I was in a lab, and I was in a pool of water."

"Lab…what Lab?"

"Well…the test tubes and everything around me said Cadmus, but some said PreClox."

"PreClox..." Martha said to herself. "Lois and Chloe, they're doing a story on PreClox, maybe they can help you, I'll get a hold of them."

"Thanks."

* * *

><p>Clark and Conner were speeding through Smallville's woodland area. They came to a stop at a rocky cavern. Clark walked inside with Conner close behind. There were drawings and symbols all over the cave walls.<p>

"Where are we?" Conner asked

"The Kawatche Caves. It was once populated by the Kawatche Indians called the Skinwalkers. My birth father had left a Kryptonian Journal here, which told of his journey here. This cave contained many Kryptonian artifacts, but now I mainly use it as a portal."

"A portal…to where?" Conner asked

Clark didn't answer, and instead walked over to a rocky altar. Clark paced a metal octagon in the center. It began to flash. In an instant, Clark and Conner began to move. Conner stood still as everything began to pass by him.

"We're teleporting." Conner said

"To my Fortress" Clark added

In an instant the two where in a large icy structure. Large ice crystals rose above their heads and pointed upward. They were surrounded by snow, and the air was cold.

"Conner this is my Fortress. The Fortress of Solitude." Clark said

"Hello, Kal-El" An accented voice said.

"Who said that?" Conner asked

"Our father, Jor-El." Clark added

"And you're Kal-El?"

"That's my real name" Clark said with a smile.

"Kal-El, I sense a visitor in our presence." Jor-El said

"Yes, Father. This is Conner…my clone, my brother."

"A new House of El member has joined us."

"Yes, father."

"Allow me to introduce him to his family."

With that a beam of light appeared around Conner. The fortress disappeared around him. Clark watched as his pupils grew, and he stood still.

* * *

><p>Conner was in a dark realm, no one before him. A man with bleached hair appeared before him. He had a white robe with the House of El symbol in black.<p>

"Hello, Conner Kent."

"Who…are you Jor-El?"

"Yes, Father of Kal-El, husband of Lara."

At that a blonde woman appeared next to him.

"Hello Conner Kent, I am Lara-El, mother of Kal-El."

"We are the parents of Kal-El, and therefore your biological parents as well."

"You are an offspring of the Kryptonian race. A race of humanoid beings advanced in the fields of science and military. Krypton was destroyed nearly 30 years ago, it's last born inhabitant being Kal-El, who was sent to Earth after days of living on his home world. Kal-El had no memory of Krypton, but was able to learn of it through the Fortress. You shall do the same."

"How about my powers? When will I learn them?"

"As a Kryptonian your powers will be discovered as you age. With each day you will become stronger, faster and more powerful than before."

"Are me and Kal-El the only Kryptonians left?"

"No. Many Kryptonians had survived Krypton's destruction. A small army of Kryptonians were able to come to Earth through a device known as The Orb, while Krypton's most dangerous criminals were placed in the Phantom Zone."

"Phantom Zone?"

"A separate dimension discovered by Jor-El, it is where they were sent in order to avoid the death sentence."

"Are me and Kal-El the last members of our family?"

"No. There is one more, but her destiny lied elsewhere."

"Who was she?"

"Kara Zor-El. The one known as Supergirl."

"Kal-El once told me he had someone there for him besides his parents, someone who helped him become a hero, who helped him embrace his Kryptonian past, was that you?"

"Yes, and we shall do that for you. Through this Fortress, you will learn to be a hero, your trials begin today."

A flash of light occurred and Conner was back in the Fortress. He looked at Clark who was waiting for him.

"…I can't believe it."

"I didn't either. You get used to it."

* * *

><p>Lois and Chloe were driving through the outskirts of Smallville, they were along the highway that connected Smallville and Edge City. As they continued to drive they came up to a massive crater in the ground. It was surrounded by heavy machinery and men in suits. They stopped Chloe's car and walked up to the window.<p>

"Ma'am, this is private property, we're going to have to request that you leave immediately."

"Sorry officer, I was just looking for the little girl's room" Lois said

"Well it's not here, so, we'll keep driving."

"We both know this isn't over"

"Of course it isn't."

As Chloe drove away, she turned back and took the key out of the ignition. She unlocked the doors and her and Lois got out. They began to sneak toward the crater. One of the guards turned around, as he heard footsteps. They hid behind a bulldozer. Chloe's phone vibrated on her side, and she saw a text message. It was from Martha.

_Lena needs your help. She's amnesiac and only remembers the past two months, we needs you to help uncover her past, we know if anyone could do it, you could. All she knows is that she was raised by Lex Luthor._

As the guard began to walk away, Lois climbed up the divers seat. She began to mess around with the buttons. As she continued to press and pull and turn the multiple peripherals, the bulldozer began to move. It began to back up away from the crater, with Chloe scrambling to keep up. The guards began to chase after it. Chloe and Lois used the distraction to their advantage, and they quickly climbed inside. Lois took out her flashlight and clicked it on. Vials of Kryptonite, blood and machinery surrounded them. The walls were burnt and electricity sparked from wires.

"I think this would fit your wall of weird."

"Definitely."

As they continued to walk by they heard footsteps. They looked to their right and saw another flash light shining at them. The light grew larger as the holder became closer. Lois jumped in front of Chloe, ready for a fight. As she pointed her flash light up she saw the face of the intruder. It was a teenage girl.

"Hey, I remember you, you where that girl me and Clark met at the reunion." Lois said

"Oh, hello Miss Lane. My name is Zoe by the way." Zoe said

"Zoe, as in the reporter for the Smallville Torch?" Chloe asked

"Yes. Why?" Zoe asked

Zoe pointed the flashlight toward Chloe's face. She had a surprised face as she saw who it was.

"Chloe Sullivan…the Chloe Sullivan. I can't believe it." Zoe said, astonished. "I have so much I have to ask you."

"How's about I go first…what exactly are you doing here?"

"Wall of Weird needed a nice story addition, and I figured who better than a CEO who faked his death. I'm pretty sure there's a much bigger story behind Lex Luthor."

"No kidding, stick with us kid, this is going to be big."

The trio turned around with their flashlights and began to walk down the Lab room. They heard nothing but the sound of their footsteps. The air was tense and quiet, and the lab was cold. As they continue to walk, they heard a rattle, and something hit Lois's leg.

"Ow!" Lois screamed. She pointed the flashlight down. It was a metal table. There were documents scattered all over. Lois passed Chloe her flashlight as she began to scramble through them. Zoe took out her camera and began to shoot photos of the documents.

"These look like records" Zoe said

"Lab records" Chloe added as she lifted them up. "LNA 1. Time of Birth is September 5th, 2011. 10:30:17 AM. Time of Death is September 5th, 2011. 12:59:01 PM. Genetic Template is…Tess Mercer."

"Tess?" Lois asked as she grabbed the document and read it over. "Lex Luthor's cloning his employees?"

"Cloning? I knew there was something behind this!" Zoe said

"Wait Zoe, Lois. There's more. LNA 2. Born the same day, died around 7 pm. Her genetic template is also Tess. She died of old age, in 3 hours. And here's one more. LNA 3. Born Septermber 6th" Chloe added

"When did she die?" Lois asked

"…It doesn't' say, it just says missing. There's something else, she was the only one to stop aging, it says biologically she's 14 years old." Chloe responded

"Wait…I see another name under genetic template. What does that say?" Zoe asked

"Kryptonian" Chloe whispered.

Chloe and Lois looked at each other, and then the three looked at the photo clipped onto her file.

"Hey…isn't that?" Chloe asked

"Lena." Zoe whispered

At that Chloe took out her phone and began taking photos of the documents. She began sending the documents to Martha. The signal was low, and the pictures took a while to send.

"Okay, we got what we needed. We should leave." Zoe said

"Yeah Chloe we need to get out of this genetic house of the dead." Lois added

As they began to walk, they heard the sound of a gun being loaded. They saw another flashlight shining at them, and then they saw the gun which was pointed at them.

"Come with me" Their captive said

* * *

><p>Martha was in the loft watching Lena who was petting one of the horses in the stable. As she sat, Shelby came up and rubbed his head against her leg. Martha began to pat his head and scratch his ears.<p>

"Good boy" She said to the golden retriever.

Her phone began to vibrate in the middle of her petting Shelby. She took her phone out of her pocket and flipped it open. She looked at the photos Chloe showed her. She gasped, as she couldn't believe what she was seeing . She got up and left Shelby on the small chair. She walked downstairs to Lena.

"Lena. Clark's friend Chloe was able to find out what you needed to know." Martha told her

"Great…what did she find out?"

Martha didn't respond, and instead she held up the phone to Lena's face. Lena squinted her eyes to see what it said, and as she began to read it she couldn't believe it. She fell on the floor and held her head.

"I'm surprised I didn't realize it earlier, you resembled her so much." Martha told her

"This is a trick." She said angrily

"I'm sorry…but it isn't." Martha appologized

"No. It's not possible. This can't be true." She said as she began to cry

"Lena…it is the truth. These are official LexCorp documents. Chloe and Lois just went into one of his defunct Labs and found them."

"No! This isn't true!" She argued "I don't believe you!"

"I'm sorry Lena. I know you don't understand it. But during my time as a Senator I've seen things like this happen before my own eyes."

"I can't be a clone…I'm a person!"

"Well, Lena…who says you can't be both? I know you don't want to accept it, but it's the truth."

Lena looked at the picture again, as she wiped the tears from her eyes. She read the names under genetic template.

"Well than tell me this. Who is Tess Mercer?"

"Tess…she's Lex Luthor's surrogate sister. After he disappeared she took control of LuthorCorp until Lex came back and renamed the company. Since then no one has seen her, but somehow Lex must have been able to get some blood or DNA if you're here."

"But why did he make me then?"

"I don't know"

"Great, so now I'm a freak. I'm some lab experiment without a family!"

"No you aren't! I know this is a lot to take in, but you better believe me when I say, you are not the first clone I've ever met! Now Lena, listen, I've seen clones that have done something with their lives. You aren't the first clone Lex Luthor has created, heck you're not even the tenth! Lex Luthor and his father lived for genetics."

"Martha…what happened to all those other clones?"

"The same things that happens to everyone else. Lena, I know you feel alone because of what you've learned. And I know you feel like you don't have a family. But that is not true. I'm here. Conner's here. We're all here for you." Martha assured her

Lena felt relief at Martha's assurance. Lena looked at the documents one last time. She read the final name under genetic template.

"But Martha…who's…Kryptonian?"

She handed Martha the phone who read the word. She looked at Lena shocked at the realization. Lena was half-Kryptonian.

* * *

><p>Clark and Conner were just returning from Clarks' Fortress. They stopped in the loft, and the two brothers looked out toward the Smallville skyline.<p>

"So me, and you, and Kara, we're the last of our family?"

"Yes, and you may not believe it but I'm actually much younger than Kara is."

"Really?"

"About 19 years. She just got suck in suspended animation, which stopped her from aging."

"Unlike me, who was stuck in accelerated aging, I'm really less than two years old, quite funny actually, you're the only one of us who aged normally."

"At least that's one thing normal" Clark said as he laughed

Shelby got up from the chair she had been resting on and rubbed herself against Clark.

"Shelby." Clark said as he began to scratch his old pet.

"I'm surprised you didn't take her with you."

"I could never do that. Shelby's someone you can't take away from Smallville. Which reminds me, I meant to do this before, but I figured, Shelby was always my trustworthy companion. The one person who accepted me as soon as we met. I figured you could use someone as loyal as she is. Conner, I'm passing her onto you. Officially." Clark said

"Thanks." Conner said with a smile.

The two brothers hugged, and Conner began to pet Shelby. Martha ran up the stair case and up to Clark.

"Clark, it's on the news. There's a hostage situation at the Metropolis Bank on Third."

"On my way. Excuse me." Clark said. As he began to walk away, he turned back and hugged Martha. He began to speed down the stairs and Martha and Conner watched out the window as Clark began to fly in his Superman suit. As he took off, he turned around and waved goodbye. Than in an instant, he was gone, a red-blue blur behind him.

"I don't know how you can enjoy knowing your going to grow up to be like him." Martha said

"Who wouldn't want to?" Conner asked

"It's a lot of responsibility." Martha added

"I'll learn to accept it." He said with a smile.

Martha smiled back, and began to walk down the stairs. As she walked down, Lena came inside and began to walk up toward Conner. As the two passed, they looked at each other.

"It'll be okay." Martha reassured her.

Lena nodded in response. She walked up to Conner.

"Hey, Conner." Lena said

"Hey" Conner replied

"Look…I need to ask you something. Conner, if you found out something about me. That made me different, very different, would you still treat me the same?" Lena asked

"I doubt there's anything that could make me see you differently. I mean after all we've been through, and we've known each other for two months. Lena, you're my best friend." Conner responded.

Lena smiled. Conner smiled back.

"Now let me ask you a question. If you learned something about me? That could change everything, everything you believe in, everything you knew possible. Would you still accept me?" Conner asked

Conner looked at Lena who looked puzzled. How much about him did she know?


End file.
